Subject: pyramidalization of amides

From: Ulrike Salzner <[email-masked]>
Date: Thu, 01 Aug 2002 12:59:10 +0300

Hello,
I am reviewing a thesis which deals with pyramidalization in amides, S, 
Se anlogues and amids in larger ring systems. Substituent effects are 
analyzed and compared with AIM and NBO. All of these systems have 
inversion barriers smaller than ammonia, some of them are planar. Thus, 
like ammonia, these molecules probably violate the Born-Oppenheimer 
approximation. How reliable are standard calculations (B3LYP/6-31G*, 
MP2/6-31G*) of bond angles, i.e. degree of pyramidalization? Should 
trends be ok? I would appreciate oppinions on this.
Sincerely,
Ulrike Salzner

---

From: "Shobe, Dave" <[email-masked]>
Date: Thu, 01 Aug 2002 12:22:34 -0400

My opinion: the calculations will be valid, if interpreted properly.  

I tend to think of such systems as "obeying" a modified, three-level
Born-Oppenheimer approximation.  In the standard two-level Born-Oppenheimer
approximation, the nuclei are frozen, with the electrons treated in quantum
mechanical fashion, giving the familiar potential energy surface.  However,
once we have that potential energy surface, we can use it to give the nuclei
a quantum treatment: that is what we do when calculating zero-point and
thermal energies.   

However, hydrogen compounds can be better treated with a three way
distinction between electrons, hydrogen nuclei (especially if they are
protons, i.e. 1H), and then the heavier nuclei.  One calculates the
potential energy surface in the usual fashion (freezing all nuclei and
allowing quantum mechanical treatment of electrons).  However, once that
potential energy surface is calculated, the hydrogen atoms would be treated
quantum mechanically while other nuclei are still frozen.  A new heavy atom
potential energy surface is thus generated, and wavefunctions and
probability distributions are calculated for the hydrogen nuclei.  There was
an article in Accounts of Chemical Research a few years ago in which this
was done for water clusters.  

Back to your question: a planar amide is still distinguished from a
pyramdialized amide in having a one-minimum or two-minima potential energy
surface for the amide hydrogen.  These produce one-maximum or two-maxima
probability distributions (respectively) for the hydrogen nuclei.
Experimental geometries typically come from diffraction studies, which
actually measure these probability distributions since the results are
averaged among the molecules in the sample.  Thus, the experimental
geometries should correspond to the minima found by B3LYP/6-31G* and the
like.

--David Shobe
Süd-Chemie Inc.
phone (502) 634-7409
fax     (502) 634-7724
email  [email-masked]

Don't bother flaming me: I'm behind a firewall.

-----Original Message-----
From: Ulrike Salzner [mailto:[email-masked]]
Sent: Thursday, August 01, 2002 5:59 AM
To: [email-masked]
Subject: CCL:pyramidalization of amides

Hello,

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